--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gops_subtract.py	Tue Apr 01 10:52:51 2014 -0400
@@ -0,0 +1,96 @@
+#!/usr/bin/env python
+"""
+Find regions of first interval file that do not overlap regions in a second
+interval file. Interval files can either be BED or GFF format.
+
+usage: %prog interval_file_1 interval_file_2 out_file
+    -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
+    -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
+    -m, --mincols=N: Require this much overlap (default 1bp)
+    -p, --pieces: just print pieces of second set (after padding)
+    -G, --gff1: input 1 is GFF format, meaning start and end coordinates are 1-based, closed interval
+    -H, --gff2: input 2 is GFF format, meaning start and end coordinates are 1-based, closed interval
+"""
+import sys, traceback, fileinput
+from warnings import warn
+from bx.intervals import *
+from bx.intervals.io import *
+from bx.intervals.operations.subtract import *
+from bx.cookbook import doc_optparse
+from galaxy.tools.util.galaxyops import *
+from utils.gff_util import GFFFeature, GFFReaderWrapper, convert_bed_coords_to_gff
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def main():
+    mincols = 1
+    upstream_pad = 0
+    downstream_pad = 0
+
+    options, args = doc_optparse.parse( __doc__ )
+    try:
+        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
+        chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )      
+        if options.mincols: mincols = int( options.mincols )
+        pieces = bool( options.pieces )
+        in1_gff_format = bool( options.gff1 )
+        in2_gff_format = bool( options.gff2 )
+        in_fname, in2_fname, out_fname = args
+    except:
+        doc_optparse.exception()
+
+    # Set readers to handle either GFF or default format.
+    if in1_gff_format:
+        in1_reader_wrapper = GFFReaderWrapper
+    else:
+        in1_reader_wrapper = NiceReaderWrapper
+    if in2_gff_format:
+        in2_reader_wrapper = GFFReaderWrapper
+    else:
+        in2_reader_wrapper = NiceReaderWrapper
+        
+    g1 = in1_reader_wrapper( fileinput.FileInput( in_fname ),
+                            chrom_col=chr_col_1,
+                            start_col=start_col_1,
+                            end_col=end_col_1,
+                            strand_col=strand_col_1,
+                            fix_strand=True )
+    if in1_gff_format:
+        # Subtract requires coordinates in BED format.
+        g1.convert_to_bed_coord=True
+        
+    g2 = in2_reader_wrapper( fileinput.FileInput( in2_fname ),
+                            chrom_col=chr_col_2,
+                            start_col=start_col_2,
+                            end_col=end_col_2,
+                            strand_col=strand_col_2,
+                            fix_strand=True )
+    if in2_gff_format:
+        # Subtract requires coordinates in BED format.
+        g2.convert_to_bed_coord=True
+        
+    out_file = open( out_fname, "w" )
+    try:
+        for feature in subtract( [g1,g2], pieces=pieces, mincols=mincols ):
+            if isinstance( feature, GFFFeature ):
+                # Convert back to GFF coordinates since reader converted automatically.
+                convert_bed_coords_to_gff( feature )
+                for interval in feature.intervals:
+                    out_file.write( "%s\n" % "\t".join( interval.fields ) )
+            elif isinstance( feature, GenomicInterval ):
+                out_file.write( "%s\n" % "\t".join( feature.fields ) )
+            else:
+                out_file.write( "%s\n" % feature )
+    except ParseError, exc:
+        out_file.close()
+        fail( "Invalid file format: %s" % str( exc ) )
+
+    out_file.close()
+
+    if g1.skipped > 0:
+        print skipped( g1, filedesc=" of 2nd dataset" )
+    if g2.skipped > 0:
+        print skipped( g2, filedesc=" of 1st dataset" )
+
+if __name__ == "__main__":
+    main()